Also see the first few sections about the config file, console, and command line if you're not familiar with that stuff.

If you're using the version of GLQuake that comes with Steam, it's kind of old/crashy (as the guide describes). Version 0.98 is available in various places like here: http://www.quaketerminus.com/nqexes/glquake098alpha.zip (throw away the opengl32.dll file from that and just use glquake.exe) ... or you could get a modern Quake engine like QuakeSpasm and much of this stuff would be easier.

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Edit: here's a quick and dirty recommendation if you want to use GLQuake 0.98. Try this set of command-line options for glquake.exe:

-width 1920 -height 1280 -conwidth 864 -conheight 486 +fov 106

(If you use the GLQuake 0.95 that comes from Steam, only width/height work, the rest of that stuff for HUD and FOV will not work.)